Hi
The JHU white matter atlases are stored in $FSLDIR/data/atlases/JHU
You can extract one of the ROIs using fslroi, for example:
fslroi JHU-ICBM-tracts-prob-2mm mytract 0 1
You can then threshold and binarise the tract using fslmaths:
fslmaths mytract -thr 20 -bin mytract_thr_bin
Cheers,
Saad.
On 23 Aug 2011, at 13:52, Amandine Pelletier wrote:
> Dear FSL users,
>
> I'm working on a cohort of 154 subjects, two types of scans were acquired : anatomical MRI and DTI scans. MD and FA indices were extracted from DTI images and analysed using Voxel-Based approach.
> I have never work with a Region Of Interest approach. My scans have already been normalized. For the moment, I have extracted values of FA in all skeleton using fslmeants :
> -i all_FA_skeletonised.nii.gz -m mean_FA_skeleton_mask.nii.gz
> Now, I would like to use the ROI which are in the atlase « JHU white-matter tractography » in order to extract values of volum, FA anf MD in the cingulum and fornix.
> I don't know how to create the mask and then how to binarise it ? With which command lines ?
>
> I'm sorry, I'm not an expert for using FSL and so I have some difficulties...
>
> Thank for your time and your help,
>
> Amandine
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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